3oe8

Crystal structure of the CXCR4 chemokine receptor in complex with a small molecule antagonist IT1t in P1 spacegroup

Method: X-RAY DIFFRACTION Dmax: 127.4 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

C-X-C chemokine receptor type 4, Lysozyme Chimera

Enterobacteria phage T4

UniProt P00720

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 1002–1161 Chain C; UniProt 1002–1161 Fragment:CXCR4 residues 2-229, LYSOZYME residues 1002-1161, CXCR4 residues 230-319 Mutation:L125W, C1054T, C1097T ITD (6,6-dimethyl-5,6-dihydroimidazo[2,1-b][1,3]thiazol-3-yl)methyl N,N'-dicyclohexylimidothiocarbamate × 2 X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;pH 6;293 K;Lipidic cubic phase made of monoolein and cholesterol, 26% PEG400, 0.3M Sodium malonate, 5mM Strontium chloride, 0.1M MES pH 6.0, LIPIDIC CUBIC PHASE, temperature 293K Resolution 3.10 Å R-free 0.295
2 Insufficient information Homooligomer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 1002–1161 Chain B; UniProt 1002–1161 Chain C; UniProt 1002–1161 Fragment:CXCR4 residues 2-229, LYSOZYME residues 1002-1161, CXCR4 residues 230-319 Mutation:L125W, C1054T, C1097T ITD (6,6-dimethyl-5,6-dihydroimidazo[2,1-b][1,3]thiazol-3-yl)methyl N,N'-dicyclohexylimidothiocarbamate × 3 X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;pH 6;293 K;Lipidic cubic phase made of monoolein and cholesterol, 26% PEG400, 0.3M Sodium malonate, 5mM Strontium chloride, 0.1M MES pH 6.0, LIPIDIC CUBIC PHASE, temperature 293K Resolution 3.10 Å R-free 0.295
3 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 1002–1161 Fragment:CXCR4 residues 2-229, LYSOZYME residues 1002-1161, CXCR4 residues 230-319 Mutation:L125W, C1054T, C1097T ITD (6,6-dimethyl-5,6-dihydroimidazo[2,1-b][1,3]thiazol-3-yl)methyl N,N'-dicyclohexylimidothiocarbamate × 1 X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;pH 6;293 K;Lipidic cubic phase made of monoolein and cholesterol, 26% PEG400, 0.3M Sodium malonate, 5mM Strontium chloride, 0.1M MES pH 6.0, LIPIDIC CUBIC PHASE, temperature 293K Resolution 3.10 Å R-free 0.295

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

721 other PDB entries and 844 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LYS_BPT4
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 242–401; UniProt 1002–1161 Author chain B; PDBConstruct 242–401; UniProt 1002–1161 Author chain C; PDBConstruct 242–401; UniProt 1002–1161

C-X-C chemokine receptor type 4, Lysozyme Chimera

Enterobacteria phage T4

UniProt P61073

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 2–229 Chain B; UniProt 230–319 Chain C; UniProt 2–229 Chain C; UniProt 230–319 Fragment:CXCR4 residues 2-229, LYSOZYME residues 1002-1161, CXCR4 residues 230-319 Mutation:L125W, C1054T, C1097T ITD (6,6-dimethyl-5,6-dihydroimidazo[2,1-b][1,3]thiazol-3-yl)methyl N,N'-dicyclohexylimidothiocarbamate × 2 X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;pH 6;293 K;Lipidic cubic phase made of monoolein and cholesterol, 26% PEG400, 0.3M Sodium malonate, 5mM Strontium chloride, 0.1M MES pH 6.0, LIPIDIC CUBIC PHASE, temperature 293K Resolution 3.10 Å R-free 0.295
2 Insufficient information Homooligomer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 2–229 Chain A; UniProt 230–319 Chain B; UniProt 2–229 Chain B; UniProt 230–319 Chain C; UniProt 2–229 Chain C; UniProt 230–319 Fragment:CXCR4 residues 2-229, LYSOZYME residues 1002-1161, CXCR4 residues 230-319 Mutation:L125W, C1054T, C1097T ITD (6,6-dimethyl-5,6-dihydroimidazo[2,1-b][1,3]thiazol-3-yl)methyl N,N'-dicyclohexylimidothiocarbamate × 3 X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;pH 6;293 K;Lipidic cubic phase made of monoolein and cholesterol, 26% PEG400, 0.3M Sodium malonate, 5mM Strontium chloride, 0.1M MES pH 6.0, LIPIDIC CUBIC PHASE, temperature 293K Resolution 3.10 Å R-free 0.295
3 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 2–229 Chain A; UniProt 230–319 Fragment:CXCR4 residues 2-229, LYSOZYME residues 1002-1161, CXCR4 residues 230-319 Mutation:L125W, C1054T, C1097T ITD (6,6-dimethyl-5,6-dihydroimidazo[2,1-b][1,3]thiazol-3-yl)methyl N,N'-dicyclohexylimidothiocarbamate × 1 X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;pH 6;293 K;Lipidic cubic phase made of monoolein and cholesterol, 26% PEG400, 0.3M Sodium malonate, 5mM Strontium chloride, 0.1M MES pH 6.0, LIPIDIC CUBIC PHASE, temperature 293K Resolution 3.10 Å R-free 0.295

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

32 other PDB entries and 32 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CXCR4_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 12–239; UniProt 2–229 Author chain A; PDBConstruct 404–493; UniProt 230–319 Author chain B; PDBConstruct 12–239; UniProt 2–229 Author chain B; PDBConstruct 404–493; UniProt 230–319 Author chain C; PDBConstruct 12–239; UniProt 2–229 Author chain C; PDBConstruct 404–493; UniProt 230–319

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 3oe8

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3oe8
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3oe8
Deposition date deposition_date2010-08-12
Structure title titleCrystal structure of the CXCR4 chemokine receptor in complex with a small molecule antagonist IT1t in P1 spacegroup
Keywords keywords;Structural Genomics, PSI-2, Protein Structure Initiative, Accelerated Technologies Center for Gene to 3D Structure, ATCG3D, 7TM, G protein-coupled receptor, GPCR, Signal transduction, Hydrolase, Cancer, HIV-1 co-receptor, chemotaxis, chemokine, CXCL12, SDF1, isothiourea, Chimera, T4L Fusion, Membrane protein, Transmembrane, SINGNALING PROTEIN, PSI-Biology, GPCR Network, SIGNALING PROTEIN ;; SIGNALING PROTEIN, HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier40.46
Radius of gyration Rg (electron density) rg_electron39.53
Forward intensity I(0) i0278331000.00
Molecular weight molecular_weight146830.0 kDa
Excluded volume excluded_volume188660 ų
Envelope volume envelope_volume265040 ų
Hydration-shell volume shell_volume56722 ų
Envelope diameter envelope_diameter131.7
Shell Rg shell_rg44.49
Envelope Rg envelope_rg38.57
Shape Rg shape_rg39.52
Total Rg total_rg39.89
Total atoms total_atoms10373
Residues n_residues1287
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax127.4
Rg (real space) rg_real40.35
Rg uncertainty (real space) rg_real_error1.09
I(0) (real space) i0_real2.7830e+08
I(0) uncertainty (real space) i0_real_error5.1490e+06
Rg (reciprocal space) rg_reciprocal40.46
I(0) (reciprocal space) i0_reciprocal278400000.0000
Solution quality estimate total_estimate0.8940
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary49.0
Skewness Skewness skewness0.181
Kurtosis Kurtosis kurtosis-0.502
Angular range angular_range— – 0.1950 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha16930000.0000
Real-space data points n_real_points40
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.947; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.776

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id3oe8A01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1070 — Rhopdopsin 7-helix transmembrane proteins
Homologous superfamily homologous superfamily10 — Rhodopsin 7-helix transmembrane proteins
Domain ID domain_id3oe8A02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily40
Domain ID domain_id3oe8B01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1070 — Rhopdopsin 7-helix transmembrane proteins
Homologous superfamily homologous superfamily10 — Rhodopsin 7-helix transmembrane proteins
Domain ID domain_id3oe8B02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily40
Domain ID domain_id3oe8C01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1070 — Rhopdopsin 7-helix transmembrane proteins
Homologous superfamily homologous superfamily10 — Rhodopsin 7-helix transmembrane proteins
Domain ID domain_id3oe8C02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily40

8. Citations (1)

9. Files and Curves (10)